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Illuminator Data Extractor

About this program

The Illuminator_data_extractor program was designed to convert various output data file formats generated by an Illumina clonal sequencer to a format that Illuminator can process. While Illuminator itself can analyse files in the fasta, _seq.txt and _qseq.txt file formats, it was decided for logistical reasons to separate the task of data analysis from the task of file formatting. Therefore this data extraction program will be updated in response to changes in Illumina output file formats, while Illuminator will be updated in response to other changes such as increased read length.

It was also decided to concentrate on the formats used by sequence files that have not been subjected to quality scoring by comparison of the reads to a reference sequence. This is because some of the capabilities for which Illuminator was designed (such as detection of rare sequence variants, and the processing of pooled samples identified by 5’-end tags) would be adversely affected by such comparison. For example, reads containing genuine sequence variants (or 5' tags) might be rejected by the Illumina pipeline because of their poor match to the reference genome sequence. It would then be impossible for any subsequent alignment method to perform sequence variant detection with better sensitivity than that achieved by the pipeline.

insilicase icon This program is still under development; however it can be downloaded along with a user guide from here on my departmental webpage. A copy of the user guide is also kept on this site here.

Computer requirements

This program runs on Microsoft Windows, using the .NET 2.0 environment which can be obtained from here.

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